There are a number of distinct microbiomes associated with living organisms. Generally, healthy microbiomes have one or more dominant bacterial species. Conversely, a number of diseases or disorders are associated with perturbed bacterial populations within microbiomes when, for example, the prevalence of one or more non-dominant species increases, lowering the relative content of the dominant species associated with good microbial health. Rapid and economical detection, identification, and/or quantification of species within a microbiome are important aspects of disease diagnosis and prognosis.